Published March 19, 2024 | Version v1
Presentation Open

BioExcel Webinar #77: Enhanced sampling in collective variable space using the Colvars library in GROMACS

  • 1. ROR icon National Institutes of Health
  • 2. ROR icon French National Centre for Scientific Research

Description

Molecular dynamics (MD) simulations are limited by their accessible time scales, and their predictive power varies greatly with the particular problem.  To overcome this limitation, MD simulations can be accelerated by means of enhanced-sampling schemes, many of which use collective variables to quantify the progress toward hard-to-reach states.  The “Colvars” (1) library is a widely used software package that implements a broad variety of collective variable-based schemes.  Beginning with the GROMACS 2024 release series, Colvars is now included in the standard GROMACS distribution, greatly simplifying its use in a simulation.  This webinar will briefly introduce the features of Colvars, and discuss them alongside other GROMACS features that are complemented or enhanced by Colvars. We will also present an interactive workflow for exploring collective variable space and preparing Colvars/GROMACS simulations using a VMD extension, the Colvars Dashboard.

(1) https://colvars.github.io/

Files

BioExcel_webinar_19032024_zenodo.pdf

Files (1.5 MB)

Name Size Download all
md5:6314bc7d71984903769c7df375844243
1.5 MB Preview Download

Additional details

Funding

BioExcel-3 – BioExcel Centre of Excellence for Computational Biomolecular Research 101093290
European Commission